add option to ignore convergence check for vasp/contcar (#355)

it is the realization for discussion #350.

Signed-off-by: Pan Xiang <[email protected]>

Author: panxiang126

dpdata/fhi_aims/output.py

@@ -1,5 +1,6 @@
 import numpy as np
 import re
+import warnings
 
 latt_patt="\|\s+([0-9]{1,}[.][0-9]*)\s+([0-9]{1,}[.][0-9]*)\s+([0-9]{1,}[.][0-9]*)"
 pos_patt_first="\|\s+[0-9]{1,}[:]\s\w+\s(\w+)(\s.*[-]?[0-9]{1,}[.][0-9]*)(\s+[-]?[0-9]{1,}[.][0-9]*)(\s+[-]?[0-9]{1,}[.][0-9]*)"
@@ -63,7 +64,7 @@ def get_fhi_aims_block(fp) :
             return blk
     return blk
 
-def get_frames (fname, md=True, begin = 0, step = 1) :
+def get_frames (fname, md=True, begin = 0, step = 1, convergence_check=True) :
     fp = open(fname)
     blk = get_fhi_aims_block(fp)
     ret = get_info(blk, type_idx_zero = True)
@@ -78,6 +79,7 @@ def get_frames (fname, md=True, begin = 0, step = 1) :
     all_virials = []    
 
     cc = 0
+    rec_failed = []
     while len(blk) > 0 :
         if debug:
            with open(str(cc),'w') as f:
@@ -87,9 +89,9 @@ def get_frames (fname, md=True, begin = 0, step = 1) :
                 coord, _cell, energy, force, virial, is_converge = analyze_block(blk, first_blk=True, md=md)
             else:
                 coord, _cell, energy, force, virial, is_converge = analyze_block(blk, first_blk=False)
-            if is_converge : 
-                if len(coord) == 0:
-                    break
+            if len(coord) == 0:
+                break
+            if is_converge or not convergence_check: 
                 all_coords.append(coord)
 
                 if _cell:
@@ -101,9 +103,16 @@ def get_frames (fname, md=True, begin = 0, step = 1) :
                 all_forces.append(force)
                 if virial is not None :
                     all_virials.append(virial)
+            if not is_converge:
+                rec_failed.append(cc+1)
+                
         blk = get_fhi_aims_block(fp)
         cc += 1
 
+    if len(rec_failed) > 0 :
+        prt = "so they are not collected." if convergence_check else "but they are still collected due to the requirement for ignoring convergence checks."
+        warnings.warn(f"The following structures were unconverged: {rec_failed}; "+prt)
+        
     if len(all_virials) == 0 :
         all_virials = None
     else :

dpdata/plugins/fhi_aims.py

@@ -4,7 +4,7 @@
 @Format.register("fhi_aims/md")
 @Format.register("fhi_aims/output")
 class FhiMDFormat(Format):
-    def from_labeled_system(self, file_name, md=True, begin = 0, step = 1, **kwargs):
+    def from_labeled_system(self, file_name, md=True, begin = 0, step = 1, convergence_check=True, **kwargs):
         data = {}
         data['atom_names'], \
             data['atom_numbs'], \
@@ -14,7 +14,7 @@ def from_labeled_system(self, file_name, md=True, begin = 0, step = 1, **kwargs)
             data['energies'], \
             data['forces'], \
             tmp_virial, \
-            = dpdata.fhi_aims.output.get_frames(file_name, md = md, begin = begin, step = step)
+            = dpdata.fhi_aims.output.get_frames(file_name, md = md, begin = begin, step = step, convergence_check=convergence_check)
         if tmp_virial is not None :
             data['virials'] = tmp_virial
         return data

dpdata/plugins/pwmat.py

@@ -11,7 +11,7 @@
 @Format.register("pwmat/output")
 class PwmatOutputFormat(Format):
     @Format.post("rot_lower_triangular")
-    def from_labeled_system(self, file_name, begin=0, step=1, **kwargs):
+    def from_labeled_system(self, file_name, begin=0, step=1, convergence_check=True, **kwargs):
         data = {}
         data['atom_names'], \
             data['atom_numbs'], \
@@ -21,7 +21,7 @@ def from_labeled_system(self, file_name, begin=0, step=1, **kwargs):
             data['energies'], \
             data['forces'], \
             tmp_virial \
-            = dpdata.pwmat.movement.get_frames(file_name, begin=begin, step=step)
+            = dpdata.pwmat.movement.get_frames(file_name, begin=begin, step=step, convergence_check=convergence_check)
         if tmp_virial is not None:
             data['virials'] = tmp_virial
         # scale virial to the unit of eV

dpdata/plugins/vasp.py

@@ -54,7 +54,7 @@ def to_system(self, data, frame_idx=0, **kwargs):
 @Format.register("vasp/outcar")
 class VASPOutcarFormat(Format):
     @Format.post("rot_lower_triangular")
-    def from_labeled_system(self, file_name, begin=0, step=1, **kwargs):
+    def from_labeled_system(self, file_name, begin=0, step=1, convergence_check=True, **kwargs):
         data = {}
         ml = kwargs.get("ml", False)
         data['atom_names'], \
@@ -65,7 +65,7 @@ def from_labeled_system(self, file_name, begin=0, step=1, **kwargs):
             data['energies'], \
             data['forces'], \
             tmp_virial, \
-            = dpdata.vasp.outcar.get_frames(file_name, begin=begin, step=step, ml=ml)
+            = dpdata.vasp.outcar.get_frames(file_name, begin=begin, step=step, ml=ml, convergence_check=convergence_check)
         if tmp_virial is not None:
             data['virials'] = tmp_virial
         # scale virial to the unit of eV

dpdata/pwmat/movement.py

@@ -1,5 +1,6 @@
 import numpy as np
 from ..periodic_table import ELEMENTS
+import warnings
 
 def system_info (lines, type_idx_zero = False) :
     atom_names = []
@@ -49,7 +50,7 @@ def get_movement_block(fp) :
     return blk
 
 # we assume that the force is printed ...
-def get_frames (fname, begin = 0, step = 1) :
+def get_frames (fname, begin = 0, step = 1, convergence_check=True) :
     fp = open(fname)
     blk = get_movement_block(fp)
 
@@ -64,20 +65,28 @@ def get_frames (fname, begin = 0, step = 1) :
     all_virials = []    
 
     cc = 0
+    rec_failed = []
     while len(blk) > 0 :
         if cc >= begin and (cc - begin) % step == 0 :
             coord, cell, energy, force, virial, is_converge = analyze_block(blk, ntot, nelm)
-            if is_converge : 
-                if len(coord) == 0:
-                    break
+            if len(coord) == 0:
+                break
+            if is_converge or not convergence_check:
                 all_coords.append(coord)
                 all_cells.append(cell)
                 all_energies.append(energy)
                 all_forces.append(force)
                 if virial is not None :
                     all_virials.append(virial)
+            if not is_converge:
+                rec_failed.append(cc+1)
+        
         blk = get_movement_block(fp)
         cc += 1
+    
+    if len(rec_failed) > 0 :
+        prt = "so they are not collected." if convergence_check else "but they are still collected due to the requirement for ignoring convergence checks."
+        warnings.warn(f"The following structures were unconverged: {rec_failed}; "+prt)
 
     if len(all_virials) == 0 :
         all_virials = None

dpdata/system.py

@@ -176,6 +176,7 @@ def __init__ (self,
                   begin = 0,
                   step = 1,
                   data = None,
+                  convergence_check = True,
                   **kwargs) :
         """
         Constructor
@@ -192,14 +193,49 @@ def __init__ (self,
                 - ``deepmd/raw``: deepmd-kit raw
                 - ``deepmd/npy``: deepmd-kit compressed format (numpy binary)
                 - ``vasp/poscar``: vasp POSCAR
+                - ``vasp/contcar``: vasp contcar
+                - ``vasp/string``: vasp string
+                - ``vasp/outcar``: vasp outcar
+                - ``vasp/xml``: vasp xml
                 - ``qe/cp/traj``: Quantum Espresso CP trajectory files. should have: file_name+'.in' and file_name+'.pos'
                 - ``qe/pw/scf``: Quantum Espresso PW single point calculations. Both input and output files are required. If file_name is a string, it denotes the output file name. Input file name is obtained by replacing 'out' by 'in' from file_name. Or file_name is a list, with the first element being the input file name and the second element being the output filename.
                 - ``abacus/scf``: ABACUS pw/lcao scf. The directory containing INPUT file is required. 
                 - ``abacus/md``: ABACUS pw/lcao MD. The directory containing INPUT file is required.
-                - ``abacus/relax``: ABACUS pw/lcao relax or cell-relax. The directory containing INPUT file is required. 
+                - ``abacus/relax``: ABACUS pw/lcao relax or cell-relax. The directory containing INPUT file is required.
+                - ``abacus/stru``: abacus stru
+                - ``abacus/lcao/scf``: abacus lcao scf
+                - ``abacus/pw/scf``: abacus pw scf
+                - ``abacus/lcao/md``: abacus lcao md
+                - ``abacus/pw/md``: abacus pw md
+                - ``abacus/lcao/relax``: abacus lcao relax
+                - ``abacus/pw/relax``: abacus pw relax
                 - ``siesta/output``: siesta SCF output file
                 - ``siesta/aimd_output``: siesta aimd output file
                 - ``pwmat/atom.config``: pwmat atom.config
+                - ``pwmat/movement``: pwmat movement
+                - ``pwmat/output``: pwmat output
+                - ``pwmat/mlmd``: pwmat mlmd
+                - ``pwmat/final.config``: pwmat final.config
+                - ``quip/gap/xyz_file``: quip gap xyz_file
+                - ``quip/gap/xyz``: quip gap xyz
+                - ``fhi_aims/output``: fhi_aims output
+                - ``fhi_aims/md``: fhi_aims md
+                - ``fhi_aims/scf``: fhi_aims scf
+                - ``pymatgen/structure``: pymatgen structure
+                - ``pymatgen/molecule``: pymatgen molecule
+                - ``pymatgen/computedstructureentry``: pymatgen computedstructureentry
+                - ``amber/md``: amber md
+                - ``sqm/out``: sqm out
+                - ``sqm/in``: sqm in
+                - ``ase/structure``: ase structure
+                - ``gaussian/log``: gaussian log
+                - ``gaussian/md``: gaussian md
+                - ``gaussian/gjf``: gaussian gjf
+                - ``deepmd/comp``: deepmd comp
+                - ``deepmd/hdf5``: deepmd hdf5
+                - ``gromacs/gro``: gromacs gro
+                - ``cp2k/aimd_output``: cp2k aimd_output
+                - ``cp2k/output``: cp2k output
         type_map : list of str
             Needed by formats lammps/lmp and lammps/dump. Maps atom type to name. The atom with type `ii` is mapped to `type_map[ii]`.
             If not provided the atom names are assigned to `'Type_1'`, `'Type_2'`, `'Type_3'`...
@@ -208,7 +244,9 @@ def __init__ (self,
         step : int
             The number of skipped frames when loading MD trajectory.
         data : dict
-             The raw data of System class.
+            The raw data of System class.
+        convergence_check : boolean
+            Whether to request a convergence check.
         """
         self.data = {}
         self.data['atom_numbs'] = []
@@ -224,7 +262,7 @@ def __init__ (self,
             return
         if file_name is None :
             return
-        self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step, **kwargs)
+        self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step, convergence_check=convergence_check, **kwargs)
 
         if type_map is not None:
             self.apply_type_map(type_map)

dpdata/vasp/outcar.py

@@ -1,5 +1,6 @@
 import numpy as np
 import re
+import warnings
 
 def system_info(lines, type_idx_zero = False):
     atom_names = []
@@ -52,7 +53,7 @@ def get_outcar_block(fp, ml = False):
     return blk
 
 # we assume that the force is printed ...
-def get_frames(fname, begin = 0, step = 1, ml = False):
+def get_frames(fname, begin = 0, step = 1, ml = False, convergence_check=True):
     fp = open(fname)
     blk = get_outcar_block(fp)
 
@@ -66,22 +67,29 @@ def get_frames(fname, begin = 0, step = 1, ml = False):
     all_virials = []    
 
     cc = 0
+    rec_failed = []
     while len(blk) > 0 :
         if cc >= begin and (cc - begin) % step == 0 :
             coord, cell, energy, force, virial, is_converge = analyze_block(blk, ntot, nelm, ml)
-            if is_converge : 
-                if len(coord) == 0:
-                    break
+            if len(coord) == 0:
+                break
+            if is_converge or not convergence_check: 
                 all_coords.append(coord)
                 all_cells.append(cell)
                 all_energies.append(energy)
                 all_forces.append(force)
                 if virial is not None :
                     all_virials.append(virial)
+            if not is_converge:
+                rec_failed.append(cc+1)
 
         blk = get_outcar_block(fp, ml)
         cc += 1
-
+    
+    if len(rec_failed) > 0 :
+        prt = "so they are not collected." if convergence_check else "but they are still collected due to the requirement for ignoring convergence checks."
+        warnings.warn(f"The following structures were unconverged: {rec_failed}; "+prt)
+        
     if len(all_virials) == 0 :
         all_virials = None
     else :